The Sphagnome Project: Enabling Ecological and Evolutionary Insights

Forum Viewpoints Here we argue that the genus Sphagnum (peat moss) represents The Sphagnome Project: enabling an unparalleled model system for ecological and evolutionary genomics, empowered by its contribution to global carbon cycling ecological and evolutionary and emerging genomic resources. Sphagnum species play a major insights through a genus-level role in peatland formation, a prime example of ecosystem engineering, whereby the organism manipulates its surrounding sequencing project habitat. Sphagnum primary production influences carbon and nutrient cycling, such as methane production and soil carbon storage, in many boreal forests and peatlands (Turetsky et al., 2012). Sphagnum ecosystem engineering involves the accumula- Summary tion of peat that facilitates its own growth while making the surrounding environment hostile for vascular plants (van Breemen, Considerable progress has been made in ecological and evolutionary 1995). Ultimately these multi-level processes lead to the formation genetics with studies demonstrating how genes underlying plant of peatlands that occupy nearly 3% of the land surface and store and microbial traits can influence adaptation and even ‘extend’ to 25% of the world’s soil carbon as recalcitrant peat (Yu et al., 2010). influence community structure and ecosystem level processes. The latter point has led to the assertion that Sphagnum has a greater Progress in this area is limited to model systems with deep genetic impact on global carbon fluxes, and therefore climate, than and genomic resources that often have negligible ecological impact any other single genus of plants (Clymo & Hayward, 1982; van or interest. Thus, important linkages between genetic adaptations Breemen, 1995). and their consequences at organismal and ecological scales are often The Sphagnum sequencing project provides a novel nonfood lacking. Here we introduce the Sphagnome Project, which incor- crop or nonbioenergy feedstock example for a plant-based genome porates genomics into a long-running history of Sphagnum research sequencing project aimed specifically at carbon cycling. The project that has documented unparalleled contributions to peatland ecol- is developing resources for within-species genetic associations with ogy, carbon sequestration, biogeochemistry, microbiome research, ecologically relevant functional traits, and the extension of those niche construction, and ecosystem engineering. The Sphagnome gene-to-trait relationships to additional species within the Project encompasses a genus-level sequencing effort that repre- Sphagnum genus. We refer to this effort collectively as the sents a new type of model system driven not only by genetic Sphagnome Project. In the following sections, we provide a brief tractability, but by ecologically relevant questions and hypotheses. introduction to the ecology and evolution of this unique plant genus. We then outline a research roadmap that highlights scientific questions relevant to the disclosure and use of a genus-wide genomic resource for Sphagnum in two major areas of distinct but overlapping research: (1) carbon sequestration and global biogeochemistry; and (2) niche construction, ecosystem engineering, and Introduction microbial associations. We demonstrate that the Sphagnome The discovery, characterization, and prediction of genes associated Project is an example of a novel model system aimed at addressing with traits, and how those traits influence ecosystem function, are ecologically relevant questions and hypotheses across levels of key challenges, especially in the face of changing climatic organizations. conditions (Whitham et al., 2006). Climate-driven alteration of biological processes occurs across all levels of organization, and is Sphagnum ecology and evolution expected to impact a wide range of ecosystem goods and services including biodiversity, nutrient cycling, climate feedback regula- Functional traits and ecosystem function tion, and productivity (Rockstr€om et al., 2009). However, our ability to associate genes with traits of ecological interest is generally Sphagnum has a remarkable ability to create and then uniquely restricted to plant model systems primarily developed for crop and thrive in nutrient-poor, acidic, and waterlogged conditions. The bioenergy feedstocks, and further limited by the sheer complexity suite of morphological, physiological, and life history traits that of applying genetic and genomic approaches to multiple species or affect Sphagnum fitness, herein termed functional traits, enable this communities. Yet the need to apply system genetic approaches in ‘ecosystem engineer’ (Jones et al., 1994) to gain a competitive complex communities is paramount as evolution takes place within advantage over other co-occurring species and therefore flourish a complex web of genetic interactions among species (Whitham under relatively harsh environmental conditions. For example, the et al., 2006). ability of Sphagnum to store and transport water is controlled 16 New Phytologist (2018) 217: 16–25 Ó 2017 UT-Battelle www.newphytologist.com New Phytologist Ó 2017 New Phytologist Trust New Phytologist Viewpoints Forum 17 largely by three distinct morphological adaptations – branching the Sphagnum cells die (Hayward & Clymo, 1983). From there architecture, leaf size and arrangement on branches, and hyaline down to the water table the carpet structure is permeable to water cells (Fig. 1a,b; Rydin & Jeglum, 2013). These traits differ and gases (particularly oxygen) and the damp plant substrates begin considerably among species, and are associated with highly to decay in this oxic zone, termed the acrotelm (Ingram, 1978; partitioned microhabitat preferences where Sphagnum species Clymo & Hayward, 1982). The consequent loss of stem strength coexist within a peatland. Hummock-forming species, growing and increasing weight eventually result in collapse of the plant c. > 30 cm above the water table, have small close-set leaves forming structure. This reduces the pore size so water can no longer flow numerous interconnected small capillary spaces (Fig. 1). Spreading easily through it, and from this point downwards the peat is branches allow lateral movement of water through the capillary permanently waterlogged and this is what determines the depth of continuum, while numerous close-set pendant branches appressed the water table. In this waterlogged zone, oxygen is consumed by to the stem form an efficient vertical water-transport system. aerobic respiration more rapidly than it can be replenished by Consequently, Sphagnum species growing on hummocks can wick diffusion (which is 10 000 times slower in water than it is in air), moisture and maintain metabolic activity even during drought creating the anoxic catotelm (Clymo, 1983). Hence, through (Rice & Giles, 1996). In all species, dead hyaline cells in the leaves distinct traits, Sphagnum generates environmental conditions that and the outer cortex of the stems and branches act as water-storage are suitable for its own growth but hostile for the vast majority of structures. other plants (e.g. van Breemen, 1995; Rydin & Jeglum, 2013). The capitula at the top of the stems are alive, but a few (c.5) The mechanisms by which Sphagnum inhibits fungal and microbial centimeters down 99% of the light has been absorbed and most of decomposition – and hence promotes peat accumulation – are not Fig. 1 Morphological traits of Sphagnum. Left panel, four representative species (modified from Crum, 1984). (a) Plant habits showing differences in branch density. (b) Branch leaf cross-sections showing arrangements of larger hyaline cells. As in most mosses, Sphagnum leaves consist of a single layer of cells, but unlike in other mosses, the leaf cells are dimorphic, comprising large hyaline cells, dead and empty at maturity, alternating with narrow photosynthetic chlorophyllose cells. In some species (e.g. top), those chlorophyllose cells are not exposed at the leaf surface and in other species they are exposed at the inner or outer surface. (c) Surface view of branch leaf cells, showing variously arranged pores on hyaline cells. The chlorphyllose cells are very narrow, forming a network around each hyaline cell. (d) Branch fascicles, each including so-called spreading and pendent branches. (e) Branch leaf. (f) Stem cross-section showing variously developed, sometimes enlarged outer cortex cells. Right panel, one (haploid) gametophyte plant with stalked capsules releasing spores (modified from Weston et al., 2015). Inset, detail of branch leaf cells showing differentiation of chlorophyllose and hyaline cells. Ó 2017 UT-Battelle New Phytologist (2018) 217: 16–25 New Phytologist Ó 2017 New Phytologist Trust www.newphytologist.com New 18 Forum Viewpoints Phytologist fully understood, but involve both the external environment 200–300 species, Sphagnum is by far the largest genus in the engineered by the species, as well as the internal biochemistry of its Sphagnopsida and the most important for peatlands. Sphagnum plant tissue, particularly the low nitrogen : carbon (N : C) ratio (a species share a common ancestor in the late Tertiary, a surprisingly reflection of the unusually efficient use of nitrogen in producing recent radiation considering the great antiquity of Sphagnopsida new biomass) (Bragazza et al., 2006). A passive mechanism for (Shaw et al., 2010). This recent radiation, which may have occurred intrinsic decay resistance in the oxic acrotelm layer is suggested by following the mid-Miocene climatic optimum, coincides

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